@organon-methodology/tools 0.3.0

package/dist/cli/commands/health.js

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+/**
+ * organon health — Dashboard showing coverage, validation, tokens, freshness.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { health } from '../../core/health.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const healthCommand = {
+    command: 'health',
+    describe: 'Show organon health dashboard (coverage, validation, tokens, freshness)',
+    builder: (yargs) => {
+        return yargs
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .option('detailed', {
+            describe: 'Show detailed issue breakdown',
+            type: 'boolean',
+            default: false,
+        })
+            .option('fix-suggestions', {
+            describe: 'Include fix suggestions for issues',
+            type: 'boolean',
+            default: false,
+        })
+            .example('$0 health', 'Quick health summary')
+            .example('$0 health --detailed --fix-suggestions', 'Detailed report with fixes');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await health({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            fixSuggestions: args['fix-suggestions'],
+        });
+        const scoreColor = result.score >= 80 ? chalk.green : result.score >= 50 ? chalk.yellow : chalk.red;
+        console.log(chalk.blue('Organon Health Dashboard'));
+        console.log();
+        console.log(`  Score: ${scoreColor(`${result.score}/100`)}`);
+        console.log();
+        // Coverage
+        console.log(chalk.dim('  Coverage:'));
+        console.log(`    ${result.coverage.withFrontmatter}/${result.coverage.totalFiles} files have frontmatter (${result.coverage.percentage}%)`);
+        // Validation
+        console.log(chalk.dim('  Validation:'));
+        console.log(`    ${chalk.green(`${result.validation.passing} passing`)}  ${result.validation.failing > 0 ? chalk.red(`${result.validation.failing} failing`) : ''}  ${result.validation.warnings > 0 ? chalk.yellow(`${result.validation.warnings} warnings`) : ''}`);
+        // Tokens
+        console.log(chalk.dim('  Tokens:'));
+        console.log(`    Total: ${result.tokens.total.toLocaleString()} | Average: ${result.tokens.average.toLocaleString()}`);
+        if (result.tokens.largest.file) {
+            console.log(`    Largest: ${result.tokens.largest.file} (${result.tokens.largest.tokens.toLocaleString()})`);
+        }
+        // Freshness
+        console.log(chalk.dim('  Freshness:'));
+        console.log(`    ${chalk.green(`${result.freshness.fresh} fresh`)}  ${result.freshness.stale > 0 ? chalk.yellow(`${result.freshness.stale} stale`) : ''}  ${result.freshness.unknown > 0 ? chalk.dim(`${result.freshness.unknown} unknown`) : ''}`);
+        // Issues (detailed mode)
+        if (args.detailed && result.issues.length > 0) {
+            console.log();
+            console.log(chalk.dim('  Issues:'));
+            for (const issue of result.issues) {
+                const prefix = issue.severity === 'error' ? chalk.red('    ✗') : chalk.yellow('    ⚠');
+                console.log(`${prefix} [${issue.code}] ${issue.message}`);
+                if (issue.suggestion) {
+                    console.log(chalk.dim(`      → ${issue.suggestion}`));
+                }
+            }
+        }
+        console.log();
+    },
+};
+//# sourceMappingURL=health.js.map

package/dist/cli/commands/health.js.map

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package/dist/cli/commands/init.d.ts

@@ -0,0 +1,14 @@
+/**
+ * organon init — Bootstrap a new project with Organon structure.
+ */
+import type { CommandModule } from 'yargs';
+interface InitArgs {
+    'target-dir': string;
+    skills: boolean;
+    force: boolean;
+    'dry-run': boolean;
+    format: string;
+}
+export declare const initCommand: CommandModule<{}, InitArgs>;
+export {};
+//# sourceMappingURL=init.d.ts.map

package/dist/cli/commands/init.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/init.js

@@ -0,0 +1,132 @@
+/**
+ * organon init — Bootstrap a new project with Organon structure.
+ */
+import * as fs from 'node:fs/promises';
+import * as path from 'node:path';
+import chalk from 'chalk';
+import { init } from '../../core/init.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const initCommand = {
+    command: 'init [target-dir]',
+    describe: 'Bootstrap a new project with Organon structure and skills',
+    builder: (yargs) => {
+        return yargs
+            .positional('target-dir', {
+            describe: 'Target directory (defaults to current directory)',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('skills', {
+            describe: 'Install Claude Code skills',
+            type: 'boolean',
+            default: true,
+        })
+            .option('force', {
+            describe: 'Overwrite existing files',
+            type: 'boolean',
+            default: false,
+        })
+            .option('dry-run', {
+            describe: 'Show what would be created without writing',
+            type: 'boolean',
+            default: false,
+        })
+            .option('format', {
+            describe: 'Output format',
+            type: 'string',
+            choices: ['human', 'json'],
+            default: 'human',
+        })
+            .example('$0 init', 'Initialize current directory')
+            .example('$0 init ./my-project', 'Initialize a specific directory')
+            .example('$0 init --dry-run', 'Preview what would be created')
+            .example('$0 init --no-skills', 'Skip skill installation');
+    },
+    handler: async (args) => {
+        const targetDir = path.resolve(args['target-dir']);
+        const nodeFs = new NodeFileSystem();
+        const result = await init({
+            projectRoot: targetDir,
+            installSkills: args.skills,
+            force: args.force,
+            fs: nodeFs,
+        });
+        // JSON output
+        if (args.format === 'json') {
+            const jsonResult = {
+                success: result.success,
+                targetDir,
+                dryRun: args['dry-run'],
+                files: [...result.files.keys()],
+                skipped: result.skipped,
+                diagnostics: result.diagnostics,
+            };
+            console.log(JSON.stringify(jsonResult, null, 2));
+            if (!result.success)
+                process.exit(1);
+            return;
+        }
+        // Human output
+        console.log(chalk.blue('Organon Init'));
+        console.log();
+        if (args['dry-run']) {
+            console.log(chalk.yellow('Dry run — no files will be written'));
+            console.log();
+        }
+        // Show files to create
+        if (result.files.size > 0) {
+            console.log(chalk.green(args['dry-run'] ? 'Files to create:' : 'Files created:'));
+            for (const filePath of result.files.keys()) {
+                console.log(`  ${chalk.green('+')} ${filePath}`);
+            }
+        }
+        // Show skipped files
+        if (result.skipped.length > 0) {
+            console.log();
+            console.log(chalk.dim(`Skipped (already exist):`));
+            for (const filePath of result.skipped) {
+                console.log(`  ${chalk.dim('-')} ${filePath}`);
+            }
+        }
+        // Actually write files (unless dry-run)
+        if (!args['dry-run'] && result.files.size > 0) {
+            const writeErrors = [];
+            for (const [relativePath, content] of result.files) {
+                try {
+                    const fullPath = path.join(targetDir, relativePath);
+                    await fs.mkdir(path.dirname(fullPath), { recursive: true });
+                    await fs.writeFile(fullPath, content, 'utf-8');
+                }
+                catch (err) {
+                    writeErrors.push(`${relativePath}: ${err instanceof Error ? err.message : String(err)}`);
+                }
+            }
+            if (writeErrors.length > 0) {
+                console.log();
+                console.log(chalk.red('Write errors:'));
+                for (const e of writeErrors) {
+                    console.log(chalk.red(`  ${e}`));
+                }
+                process.exit(1);
+            }
+        }
+        // Summary
+        console.log();
+        if (result.files.size === 0) {
+            console.log(chalk.dim('No files to create. Project is already initialized.'));
+            console.log(chalk.dim('Use --force to overwrite existing files.'));
+        }
+        else if (args['dry-run']) {
+            console.log(chalk.yellow(`Would create ${result.files.size} file(s). Run without --dry-run to apply.`));
+        }
+        else {
+            console.log(chalk.green(`Created ${result.files.size} file(s).`));
+            console.log();
+            console.log(chalk.blue('Next steps:'));
+            console.log(`  1. Edit ${chalk.bold('organon/ETHOS.md')} — define your project's identity and constraints`);
+            console.log(`  2. Edit ${chalk.bold('organon/PHILOSOPHY.md')} — document your design rationale`);
+            console.log(`  3. Run ${chalk.bold('organon verify')} — check project integrity`);
+        }
+    },
+};
+//# sourceMappingURL=init.js.map

package/dist/cli/commands/init.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/mcp.d.ts

@@ -0,0 +1,11 @@
+/**
+ * organon mcp — Start the MCP server (stdio transport).
+ */
+import type { CommandModule } from 'yargs';
+interface McpArgs {
+    'project-root': string;
+    config?: string;
+}
+export declare const mcpCommand: CommandModule<{}, McpArgs>;
+export {};
+//# sourceMappingURL=mcp.d.ts.map

package/dist/cli/commands/mcp.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"mcp.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/mcp.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAC;AAG3C,UAAU,OAAO;IACf,cAAc,EAAE,MAAM,CAAC;IACvB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,EAAE,EAAE,OAAO,CAuBjD,CAAC"}

package/dist/cli/commands/mcp.js

@@ -0,0 +1,26 @@
+/**
+ * organon mcp — Start the MCP server (stdio transport).
+ */
+export const mcpCommand = {
+    command: 'mcp',
+    describe: 'Start the Organon MCP server (stdio transport)',
+    builder: (yargs) => {
+        return yargs
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .example('$0 mcp', 'Start MCP server on stdio');
+    },
+    handler: async (args) => {
+        // Dynamic import to avoid loading MCP SDK unless this command is used
+        const { startServer } = await import('../../mcp/server.js');
+        await startServer(args['project-root'], args.config);
+    },
+};
+//# sourceMappingURL=mcp.js.map

package/dist/cli/commands/mcp.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/query.d.ts

@@ -0,0 +1,19 @@
+/**
+ * organon query — Filter organon files by frontmatter metadata.
+ */
+import type { CommandModule } from 'yargs';
+interface QueryArgs {
+    'project-root': string;
+    config?: string;
+    scope?: string;
+    type?: string;
+    priority?: string;
+    task?: string;
+    budget?: number;
+    name?: string;
+    related?: string;
+    verbose?: boolean;
+}
+export declare const queryCommand: CommandModule<{}, QueryArgs>;
+export {};
+//# sourceMappingURL=query.d.ts.map

package/dist/cli/commands/query.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/query.js

@@ -0,0 +1,103 @@
+/**
+ * organon query — Filter organon files by frontmatter metadata.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { query } from '../../core/query.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const queryCommand = {
+    command: 'query',
+    describe: 'Query organon files by frontmatter metadata',
+    builder: (yargs) => {
+        return yargs
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .option('scope', {
+            describe: 'Filter by scope',
+            type: 'string',
+            choices: ['product', 'domain', 'feature', 'component', 'meta', 'methodology'],
+        })
+            .option('type', {
+            describe: 'Filter by type',
+            type: 'string',
+            choices: ['navigation', 'constraints', 'rationale', 'procedures', 'mapping'],
+        })
+            .option('priority', {
+            describe: 'Filter by load priority',
+            type: 'string',
+            choices: ['high', 'medium', 'low'],
+        })
+            .option('task', {
+            describe: 'Filter by required_for task',
+            type: 'string',
+        })
+            .option('budget', {
+            describe: 'Maximum total token budget',
+            type: 'number',
+        })
+            .option('name', {
+            describe: 'Filter by name (substring match)',
+            type: 'string',
+        })
+            .option('related', {
+            describe: 'Filter by related domain or feature',
+            type: 'string',
+        })
+            .option('verbose', {
+            describe: 'Show full file content',
+            type: 'boolean',
+            default: false,
+        })
+            .example('$0 query --scope=meta', 'List all meta-scope organons')
+            .example('$0 query --budget=20000', 'Plan context loading within 20K tokens')
+            .example('$0 query --task=genesis_tool_impl', 'Find organons for a specific task');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await query({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            scope: args.scope,
+            type: args.type,
+            priority: args.priority,
+            task: args.task,
+            budget: args.budget,
+            namePattern: args.name,
+            relatedDomain: args.related,
+            relatedFeature: args.related,
+            verbose: args.verbose,
+        });
+        console.log(chalk.blue('Organon Query'));
+        console.log();
+        if (result.files.length === 0) {
+            console.log(chalk.yellow('  No matching files found'));
+        }
+        else {
+            for (const f of result.files) {
+                const fm = f.frontmatter;
+                const tokens = fm?.token_estimate ?? '?';
+                const priority = fm?.load_priority ?? '-';
+                console.log(`  ${chalk.green(f.path)}`);
+                console.log(chalk.dim(`    ${fm?.type ?? '?'} | ${fm?.scope ?? '?'} | ${tokens} tokens | priority: ${priority}`));
+                if (fm?.summary) {
+                    console.log(chalk.dim(`    ${fm.summary}`));
+                }
+            }
+        }
+        console.log();
+        console.log(chalk.dim(`${result.files.length} file(s) | ${result.totalTokens} total tokens`));
+        for (const w of result.warnings) {
+            console.log(chalk.yellow(`  ⚠ ${w.message}`));
+        }
+    },
+};
+//# sourceMappingURL=query.js.map

package/dist/cli/commands/query.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/upgrade.d.ts

@@ -0,0 +1,13 @@
+/**
+ * organon upgrade — Detect version drift and apply updates.
+ */
+import type { CommandModule } from 'yargs';
+interface UpgradeArgs {
+    'target-dir': string;
+    apply: boolean;
+    skills: boolean;
+    format: string;
+}
+export declare const upgradeCommand: CommandModule<{}, UpgradeArgs>;
+export {};
+//# sourceMappingURL=upgrade.d.ts.map

package/dist/cli/commands/upgrade.d.ts.map

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package/dist/cli/commands/upgrade.js

@@ -0,0 +1,162 @@
+/**
+ * organon upgrade — Detect version drift and apply updates.
+ */
+import * as fs from 'node:fs/promises';
+import * as path from 'node:path';
+import chalk from 'chalk';
+import { NodeFileSystem } from '../../core/node-fs.js';
+import { detectVersion, computeUpgradePlan, applyUpgrade, } from '../../core/upgrade.js';
+export const upgradeCommand = {
+    command: 'upgrade [target-dir]',
+    describe: 'Detect version drift and upgrade project to latest methodology',
+    builder: (yargs) => {
+        return yargs
+            .positional('target-dir', {
+            describe: 'Target directory (defaults to current directory)',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('apply', {
+            describe: 'Apply all changes',
+            type: 'boolean',
+            default: false,
+        })
+            .option('skills', {
+            describe: 'Upgrade skills only',
+            type: 'boolean',
+            default: false,
+        })
+            .option('format', {
+            describe: 'Output format',
+            type: 'string',
+            choices: ['human', 'json'],
+            default: 'human',
+        })
+            .example('$0 upgrade', 'Show upgrade report (dry run)')
+            .example('$0 upgrade --apply', 'Apply all upgrades')
+            .example('$0 upgrade --apply --skills', 'Upgrade skills only');
+    },
+    handler: async (args) => {
+        const targetDir = path.resolve(args['target-dir']);
+        const nodeFs = new NodeFileSystem();
+        const shouldApply = args.apply;
+        // 1. Detect version
+        const version = await detectVersion(targetDir, nodeFs);
+        // 2. Compute plan
+        const plan = await computeUpgradePlan({
+            projectRoot: targetDir,
+            skillsOnly: args.skills,
+            fs: nodeFs,
+            version,
+        });
+        // JSON output (dry-run only — plan without apply)
+        if (args.format === 'json' && !shouldApply) {
+            const jsonResult = {
+                version: plan.version,
+                changes: plan.changes,
+                applied: false,
+            };
+            console.log(JSON.stringify(jsonResult, null, 2));
+            return;
+        }
+        // Human output
+        console.log(chalk.blue('Organon Upgrade'));
+        console.log();
+        // Version info
+        const currentLabel = version.current ?? chalk.dim('(unversioned)');
+        if (version.drift === 'none') {
+            console.log(`  Methodology: ${chalk.green(version.target)} (up to date)`);
+        }
+        else {
+            console.log(`  Methodology: ${currentLabel} → ${chalk.green(version.target)}`);
+        }
+        console.log();
+        // Changes
+        if (plan.changes.length === 0) {
+            console.log(chalk.green('  Everything is up to date. No changes needed.'));
+            return;
+        }
+        // Group by type
+        const skillChanges = plan.changes.filter((c) => c.type === 'skill');
+        const configChanges = plan.changes.filter((c) => c.type === 'config');
+        const structureChanges = plan.changes.filter((c) => c.type === 'structure');
+        if (skillChanges.length > 0) {
+            console.log(`  Skills (${skillChanges.length} change${skillChanges.length > 1 ? 's' : ''}):`);
+            for (const change of skillChanges) {
+                const icon = change.action === 'create' ? chalk.green('[N]') : chalk.yellow('[U]');
+                console.log(`    ${icon} ${change.description}`);
+            }
+            console.log();
+        }
+        if (configChanges.length > 0) {
+            console.log(`  Config (${configChanges.length} change${configChanges.length > 1 ? 's' : ''}):`);
+            for (const change of configChanges) {
+                const icon = change.action === 'create' ? chalk.green('[N]') : chalk.yellow('[U]');
+                console.log(`    ${icon} ${change.description}`);
+            }
+            console.log();
+        }
+        if (structureChanges.length > 0) {
+            console.log(`  Structure (${structureChanges.length} change${structureChanges.length > 1 ? 's' : ''}):`);
+            for (const change of structureChanges) {
+                const icon = change.action === 'create' ? chalk.green('[N]') : chalk.yellow('[U]');
+                console.log(`    ${icon} ${change.description}`);
+            }
+            console.log();
+        }
+        // Apply or show dry-run message
+        if (!shouldApply) {
+            console.log(chalk.yellow(`  ${plan.changes.length} change(s) available. Run with --apply to upgrade.`));
+            return;
+        }
+        // Apply
+        const result = await applyUpgrade(plan, targetDir, nodeFs);
+        const writeErrors = [];
+        for (const [relativePath, content] of result.filesToWrite) {
+            try {
+                const fullPath = path.join(targetDir, relativePath);
+                await fs.mkdir(path.dirname(fullPath), { recursive: true });
+                await fs.writeFile(fullPath, content, 'utf-8');
+            }
+            catch (err) {
+                writeErrors.push(`${relativePath}: ${err instanceof Error ? err.message : String(err)}`);
+            }
+        }
+        const overallSuccess = result.success && writeErrors.length === 0;
+        // JSON output for apply mode
+        if (args.format === 'json') {
+            const jsonResult = {
+                success: overallSuccess,
+                version: plan.version,
+                applied: result.applied,
+                writeErrors,
+                diagnostics: result.diagnostics,
+            };
+            console.log(JSON.stringify(jsonResult, null, 2));
+            if (!overallSuccess)
+                process.exit(1);
+            return;
+        }
+        // Human output: report write errors
+        if (writeErrors.length > 0) {
+            console.log(chalk.red('  Write errors:'));
+            for (const e of writeErrors) {
+                console.log(chalk.red(`    ${e}`));
+            }
+        }
+        // Report diagnostics
+        for (const diag of result.diagnostics) {
+            if (diag.severity === 'error') {
+                console.log(chalk.red(`  Error: ${diag.message}`));
+            }
+        }
+        if (overallSuccess) {
+            console.log(chalk.green(`  Applied ${result.applied.length} change(s).`));
+        }
+        else {
+            console.log(chalk.red(`  Upgrade completed with errors.`));
+            process.exit(1);
+        }
+    },
+};
+//# sourceMappingURL=upgrade.js.map

package/dist/cli/commands/upgrade.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/validate.d.ts

@@ -0,0 +1,13 @@
+/**
+ * organon validate — Validate organon frontmatter (4-stage validation).
+ */
+import type { CommandModule } from 'yargs';
+interface ValidateArgs {
+    'project-root': string;
+    config?: string;
+    files?: string[];
+    stages?: number[];
+}
+export declare const validateCommand: CommandModule<{}, ValidateArgs>;
+export {};
+//# sourceMappingURL=validate.d.ts.map

package/dist/cli/commands/validate.d.ts.map

@@ -0,0 +1 @@
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